Slashdot Mirror
Human Genome Contaminated With Mycoplasma DNA
KentuckyFC writes "The published human genome is contaminated with DNA sequences from mycoplasma bacteria, according to bioinformatics researchers who blame an epidemic of mycoplasma contamination in molecular biology labs around the world. The researchers say they've also found mycoplasma DNA in two commercially available human DNA chips made by biotech companies for measuring levels of human gene expression. So anybody using these chips to measure human gene expression is also unknowingly measuring mycoplasma gene expression too. The mycoplasma genes are clearly successful in reproducing themselves in silico raising the possibility that we're seeing the beginnings of an entirely new kind of landscape of infection. One option to combat this kind of virtual infection is to protect databases with the genomic version of antivirus software, a kind of virtual immune system. But this in itself could make things worse by triggering an evolutionary arms race that selects genes most capable of beating the safeguards."
...clearly uses DRM.
Haven't heard that one before...
would they wind up with Swamp Thing?
Look back up at my post, now look back down, you're on the Internet. Now look back up. I'm a signature.
I wonder exactly how far medicine has been set back by this. Researchers trying to investigate genetic or genetically-influenced diseases cannot be happy. They've unwittingly been missing information, and treating false information as valid, for a long time.
But this in itself could make things worse by triggering an evolutionary arms race that selects genes most capable of beating the safeguards.
Why is the word "evolutionary" used here? We're talking about static data that is not "executed" - it does not reproduce, it is only copied verbatim. Invalid data that bypasses filters ("antivirus software") is simply that - corrupt, invalid data that does not belong, but at least there will be less of it after filtering. That doesn't make the data somehow more powerful or adaptive - the filter merely missed it. The key fact is the data does not get to modify itself in an iterative fashion in order to survive or improve.
Better known as 318230.
At first I was relieved that this was a bacteria infecting silicon. Now I'm concerned: When will Avast release an Antibacterial beta? I'm still running Windows, folks! I know I'm vulnerable to this!!!
khasim (12/9/06): In a blind taste test, more people preferred Coke over the Pepsi that I had previously pissed in.
No resources are freed for any future generations of database contaminants to breed on by filtering. And, the notion of evolution would also require changes to the contaminants, which don't really happen. So by all means, filter. It will leave harder-to-detect contaminants there, but they won't become more numerous.
Is the human genome contaminated or is it the published sequence that is contaminated?
If only the latter, fix the title.
This was my first thought when reading the summary - there is no source of feedback to make the data filtering mechanisms loop into the evolutionary design of the bacteria involved unless - and this incredibly out there - everyone starts applying methods to kill the bacteria only based on the amount of corrupt data they scan in - then *maybe* it would be possible for those bacteria with lesser differences to make their way into the system while the rest die out, but that is incredibly unlikely given their otherwise blind nature to the whole process and the fact it would impose evolutionary constraints in direct contradiction to what makes them able to survive - not absolutely impossible, but detracting from the actual story here with such nonsensical hype would be like suggesting the same evolutionary arms race in the same situation because darth vador were to rise out of the earth's molten core to proclaim dominance over the moon, leaving some new bacteria behind on his way - it doesn't make any fucking sense.
This is really unfortunate if you intend to reproduce, as all Eukaryots pass through flagellum stage at a point of the life cycle.
Just exactly where did you go to school? Have you considered trying it again?
Faster! Faster! Faster would be better!
that part is nonsensical:
The mycoplasma genes are clearly successful in reproducing themselves in silico raising the possibility that we're seeing the beginnings of an entirely new kind of landscape of infection. One option to combat this kind of virtual infection is to protect databases with the genomic version of antivirus software, a kind of virtual immune system. But this in itself could make things worse by triggering an evolutionary arms race that selects genes most capable of beating the safeguards.
static data don't evolve
Jehovah be praised, Oracle was not selected
My understanding is that nowadays new high speed sequencing machine can get an entire human genome processed in a couple of month.
So I would think that after a couple of independent runs one should be able to flush out the non-human DNA assuming the same bacteria contamination is not ever present?
Obviously this is not a cheap endeavor but given that there is quite a bit of commercial interest in using correct human genome data this seems to me to be a worthwhile investment.
I find it puzzling that the abstract of the article does not allude to this.
How in the world will setting filters on a database put a bacteria in a lab half way around the world at an evolutionary disadvantage? The bacteria will still grow, contaminate the sample, and get sequenced, but the sequence will be rejected. There is no feedback mechanism here, no selective pressure.
Genome sequence assembly is pretty far removed from the milieu in which a bacteria must make it's way. And inadvertently including bacterial sequences on a gene expression chip is sloppy science, but hardly news.
Traditional computer viruses are the only things that truly 'reproduce' in silico. Memes are your next best option, but the 'net is just a carrier - they have to infect a human host to reproduce. Stay away from 4chan if you want to avoid infection...
But bacteria? In silico? Where are we going with this strained analogy, anyway?
-V-
Who can decide a priori? Nobody.
-Sartre
No, they're not saying that the mold itself is appearing in the chips, just that the mold's DNA is. Therefore, the presence (or absence) of the mold in a sample would skew the results when using these chips. And yes, saying that the DNA appears "in silico" is perfectly valid here - whether you care for the term or not.
For genome 3.1.
All humans save three have passed through flagellum stage. Their names were Adam, Eve, and Jesus.
This is Slashdot. You almost certainly have flagella.
# cat
Damn, my RAM is full of llamas.
So to what extent does this "epidemic of mycoplasma contamination" increase the potential for false-positives on DNA matching tests, such as used in criminal investigation or paternity cases? Does a given lab or lab-equipment manufacturer have a common strain of contamination which increases the number of "always match" markers above the threshhold defined for claiming a match?
Everybody gets what the majority deserves.
Who knew?
=^..^= all your rodent are belong to us
This is EXACTLY what happened in 70s-80s with Henrietta Lacks IMMORTAL 'HeLa' cell. http://en.wikipedia.org/wiki/HeLa
Her cells were the first Human cells to grow outside the human body.
In fact they were so successful, that unbeknown to scientists ALL OVER THE WORLD, her cells had TAKEN OVER all of the cells in their labratories GLOBALLY.
There is an amazing BBC documentary on this by Adam Curtis called "Modern Times: The Way of All Flesh"
wiki quote " Contamination: Because of their adaptation to growth in tissue culture plates, HeLa cells are sometimes difficult to control. They have proven to be a persistent laboratory "weed" that contaminates other cell cultures in the same laboratory, interfering with biological research and forcing researchers to declare many results invalid. The degree of HeLa cell contamination among other cell types is unknown because few researchers test the identity or purity of already-established cell lines. It has been demonstrated that a substantial fraction of in vitro cell lines — approximately 10%, maybe 20% — are contaminated with HeLa cells"
Almost created a COLD WAR incident:
wiki quote:-"The USSR and the USA had begun to cooperate in the war on cancer launched by President Richard Nixon only to find that the exchanged cells were contaminated by HeLa"
In the case of little Jeffery, Mycoplasma, you ARE the father!
So it would seem Evolution is favoring hackers, that breed well...
- Dan.
~ People that think they are better than anyone else for any reason are the cause of all the strife in the world.
As a career microbiologist and bioinformatics geek, the complete and utter scientific inaccuracy of this summary made me want to cry.
The mycoplasma genes are clearly successful in reproducing themselves in silico raising the possibility that we're seeing the beginnings of an entirely new kind of landscape of infection. One option to combat this kind of virtual infection is to protect databases with the genomic version of antivirus software, a kind of virtual immune system. But this in itself could make things worse by triggering an evolutionary arms race that selects genes most capable of beating the safeguards
Mycoplasma is a common contaminant of many human cell culture lines. It is often present in low counts, and is a relatively slow growing organism. This is a problem, because many of the immortal cell lines are passed serially, meaning that the mycoplasma propagates right along with it. Most labs that perform cell culture now do routine PCR testing for mycoplasma markers as a quality control measure.
When it comes to sequencing, and in particular, high-throughput next generation sequencing (Illumina/454/SOLiD/PacBio/whatever), you are shotgun sequencing all of the DNA in a given sample extract. This means that if you had a bunch of human cells, that happenned to be contaminated with low counts of mycoplasma, those mycoplasma sequences would be present to some extent in your final sequencing project. Whether this would factor into the final assembly, or just get thrown out depends on the quality control, experience of the bioinformatics team and assembly software pipeline. I am willing to be that most issues with mycoplasma contamination were during the "formative" years of high-throughput sequencing, but may have lingered in databases. These databases would in turn might used by commercial companies that build microarrays or other high-density tools, so it's feasible that some mycoplasma sequence carried over.
Is this relevant? Probably not. On a microarray, it would most likely be wasted space (eg: always negative during gene expression studies... unless the patient had a mycoplasma infection or something). Furthermore, a simple analysis of the sequence would help to rule out sequences that were clearly prokaryotic.
"In silico" does not mean what you think it means. In fact, this whole bit about in-silico replication and arms races is complete and utter nonsense. In-silico biology usually refers to biocomputing. Eg: analyzing, manipulating and simulating gene/protein sequences, expression, signalling cascades, and the like on a computer system. It does not apply to mycoplasma sequences running around all nambly pambly causing infections that would require some sort of anti-virus software. What they might be alluding to is the fact that a lot of shotgun sequencing libraries are run, as needed, through a vector screen, which is designed to pull out irrelevant sequences that may have been necessarily introduced during cloning or sequencing. Plasmids, cosmids, whatever. These algorithms may need better tuning to do a better job of ruling out mycoplasma in human sequences, but there's no danger of these mycoplasma sequencing replicating and taking over the world.
Unless you happen to be William Gibson.
This article was horribly written. They go between using terms with their literal meaning and using terms in metaphorical creative language but do not differentiate between the two using context at all. It's an incredibly confusing read. Actual ancestral human DNA is not contaminated with actual mycoplasma DNA sequences.
Here's what I gather is going on:
Researchers took a sample of human DNA and sequenced it, while doing so the sample was contaminated with DNA from mycoplasma (possibly from bacteria in the lab or on the researchers themselves). While sequencing it, the data is assumed to be a representation of pure human DNA (which would be incorrect). Other researchers then use this data set as a reference to compare other human DNA samples they sequenced themselves. They use this to test gene expression and so forth. So if their DNA samples show gene expression for mycoplasma they would incorrectly think it was normal human gene expression. What they did is use software to strip the mycoplasma DNA data from the original data set (that had both human and mycoplasma DNA sequences) to only use the actual human DNA data as a reference. The biological contamination was first in the original sample that was tested, and then the contamination referred to elsewhere is computational data "contamination." This is the software they are referring to as antivirus software and virtual immune system (which isn't antivirus software or similar to a biological immune system, it's DNA data filtering software).
These people really need to think about what they're trying to say before puking up jargon salad on the readers' brains.
I don't want to be excessively harsh but the summary was seriously a bunch of drivel. In silico either means it's data on the computer, or that you are simulating a biological process computationally. But as other posters have mentioned, unless you are purposely simulating evolution, mycoplasma sequences in your human databases isn't going to cause any "arms race." Yes, it seriously screws with validity, but that's a completely different issue.
This is a generalization, and no offense to fellow Slashdotters, but in my experience most of the computer scientists that I've met have a really crappy understanding of even basic biology. CS concepts don't directly translate to biology ones.
Cogito, ergo sum, fosho!
Try self flagellation
Myco means fungi right?
i believe the evolutionary arms race was triggered a long time ago (possibly in a galaxy far far away) /. is so full of tripe today its making me question my patronage
Were these the patented sequences?
Paranoia is a Survival Trait!
And it is EXACTLY what happened in JURASSIC PARK! The frog cells allowed some of the female dinosaurs to mutate into MALE Dinosaurs! We COULD be looking at RAPTORS who live in SILICA, and WE will ALL be typing in ALL CAPS out of sheer FEAR!
Gently reply
Bacterium, not mold. Mycoplasma is genus name of this particular bacterium.
...the future crusty old bastards are already drinking the Kool-Aid.
The whole "evolution" thing is the biggest sensationalist bullshit I've ever heard. Ignore it.
As was mentioned in another comment, it seems like the summary is misleading on the "contamination" actually being in the genome sequence.
The use of terms for sequence data and expression data are not interchangeable. The U133 microarray is for RNA, yes RNA, expression data. RNA microarrays quantify the fold change difference in expression between different subjects. DNA microarrays identify polymorphisms or repeats or the like. While arrays like the U133 rely on sequence level data to create the array, this is not the same as saying that sequence-level data is contaminated. Bottom line, the fact that this is not the cover article for Nature|Genetics this month tells you a lot of the story. Unless you are some sort of conspiracy theorist, or want to get swept up in the usual slashdot "sky is falling" imperative.
Well *I* laughed.
"All these years believing you're the signified monkey, only to find out you're just a big hunk of nobody cares."
So the arXiv article (http://arxiv.org/abs/1106.4192v1) cited in TFA is a little more accurate than the already-much-panned summary. But the authors of the arXiv article still use the term 'virtual infection' which is very misleading at best.
Basically there are a few (actually only two described in the paper) entries in one particular human genome database maintained at EMBL that appear to be mycoplasma-derived. Two out of 45,000 features on the Affymetrix Human U133 +2 oligonucleotide array, used to quantify mRNA levels in a given sample, appear to correspond to the mycoplasma sequences. So, at best, two of the genes you look at (out of 45,000) might be mycoplasma genes in that particular type of experiment.
It's not a big deal, so that's why the work isn't published in a peer-reviewed journal.
Seems there are other possibly related forms of this beast: http://www.nap.edu/openbook.php?record_id=11765&page=181
Laws are like sausages. It's better not to see them being made. - Otto von Bismarck
True. In the end, mycoplasm is just another contributing factor to signal/noise in your dataset. It's completely illusory to assume that you get noiseless measurements given the amount of data involved.
Ubi solitudinem faciunt, pacem appellant.
These guys have a lot of crap to talk. Maybe they are very idle.http://www.laserqueen.com.au/injectables.html